This help document describes the Phenotypes section of an Allele Detail report and answers the following questions:
What is the purpose of the Phenotypes section?
The purpose of the Phenotypes section is to display all genotypes involving an allele with annotations in affected anatomical systems.
In this table, you can:
- view data ordered by Mammalian Phenotype term
- associate a genotype with a color when interpreting this and the Disease models section on the Allele Detail report
- show or hide all annotated terms
- open a new window displaying each genotype's annotations (by clicking a genotype abbreviation (e.g. hm1)
- expand or contract an affected system to see specific subsystems
- locate terms in the ontological hierarchy (by following links to the Mammalian Phenotype Browser)
- examine research for the phenotypic annotations (by following links to Reference detail reports from the new window).
How do I interpret the Phenotypes section?
section begins with a Key that explains the abbreviations used in this section, the Allelic Composition, Genetic Background and Cell Lines associated with each Genotype containing the featured allele. These are followed by a matrix of the Affected Systems examined for the genotypes.
The key at the top of the Phenotype Summary by Mammalian Phenotype terms table contains one color bar for each different allelic "state" (e.g., homozygous, heterozygous).
Each state has a color, an abbreviation for the state (e.g., hm for homozygous, ht for heterozygous, and so on) and a number (arrayed sequentially) for each search result.
|cn (green)||conditional genotype|
|cx (purple)||complex (more than one genome feature)|
|tg (pink)||involves transgenes|
|ot (brown)||other: hemizygous, indeterminate...|
|N||Normal phenotype. Current annotations for this genotype and term indicate absence of abnormality. |
|∅||NOT a model for this disease, contrary to expectation. See References for details.|
|✓||There is an abnormal phenotype in the affected system. Click ► in the Affected Systems column to see the specific column annotated. Click the term name to view it in the Mammalian Phenotype Browser. |
|Blank space||No information.|
There is a number for each genotype involving this allele with annotations in affected anatomical systems. Numbers increase sequentially. If the number of genotypes in MGI involving this allele is 29, there will be 29 rows in the Key table (e.g., hm1...ht15...cx20...tg29) and 29 columns in the Affected Systems table.
|Genotype ||Genotype abbreviation (e.g., hm1, ht4) used in this web page.|
|Allelic Composition||Genotype of each allele, linked to its MGI Allele Detail report.|
|Genetic Background||Mouse strains involved, if known.|
|Cell Line(s)||Cell line(s)|
The Affected Systems column lists anatomical terms from the Mammalian Phenotypes Browser for which there are phenotypic annotations.
- If a term you are interested in does not appear, it means that, currently, there are no annotations to the term for this allele.
- The sort order is alphabetical (e.g., behavioral/neurological before cardiovascular, skeleton before skin/coat/nails).
- To expand or collapse a single system, click the ► or ▼ beside it.
Show or hide all annotated terms
|show||Click to expand or open a view of all annotations for this allele.|
|hide||Click to contract or close the annotation list.|
To see information for all check marked anatomical terms in a column (i.e., all the Affected Systems for hm1):
- Locate the header row.
- Click the genotype abbreviation in a column of interest (e.g., hm1). A new window appears, displaying all annotations from that column; links to the Mammalian Phenotype Browser (for term ontology); MGI J: numbers (for references); disease annotations (when relevant); and images (when available).
- Open as many windows as desired.
Click View phenotypes for all genotypes (concatenated display) to see all genotypes and phenotypic annotations in a single browser window.
What should appear in the Sex row?
For genotypes with sex specific data, the appropriate male or female symbol appears, indicating the phenotypic sex analyzed. If this row is missing, either sex specific data were not reported or there were no sex differences.
What should appear in the Source row?
When one of the genotypes has data from one of the high-throughput phenotyping projects, the curation source is displayed for all genotypes. WTSI (Wellcome Trust Sanger Institute) and EuPh (Europhenome Mouse Phenotyping Resource) are examples. When two sources are displayed in a column heading, such as IMPC-WTSI, the first one (in this case, the International Mouse Phenotyping Center) is the Data Interpretation Center and the second one is the Phenotyping Center (in this case the Welcome Trust Sanger Institute) that generated the data. The Interpretation Center decides whether the measured trait is significantly different from normal and assigns the appropriate phenotype terms. When only one high-throughput phenotyping project is given, the source generated the data and made the interpretations. If the Source row is missing, MGI is the curation source.
What should appear on the Affected Systems list? How is it sorted?
The Affected Systems list contains annotation terms from the Mammalian Phenotypes Browser. If a term does not appear, it means that, at this time, the MGI database does not contain annotations for this allele to the term. The sort order in the summary table is always alphabetical (e.g., behavioral/neurological before cardiovascular, skeleton before skin/coat/nails).
What's the difference between N and ∅? What does a blank cell indicate?
- N means that phenotypic analysis has occurred, and there is a report of no abnormality for part or all of the system although an abnormality was expected.
- If an N is visible when the system is closed (i.e., hide;), then only unexpected normals are annotated for that system.
- Click show or hide to investigate all research results for this (any) genotype/affected system.
- ∅, in the Disease Model section of the Allele Detail page, means that, contrary to expectation, this genotype is not a model for a specific disease or diseases.
- A blank cell indicates that, in MGI, the genotype in the column has not been annotated to the term in the row.
Where is the research that supports an annotation?
Click the column header in the Genotypes row (e.g., hm1, ht15, cx19). In the window that appears, J-numbered citations (e.g., J:7454) appear after each Mammalian Phenotype Browser term (in parentheses). Clicking a citation brings up its MGI References report. Here you will find publication details, an abstract, and links to additional MGI information.
When there is more than one reference paper, bullet items beneath the Mammalian Phenotype vocabulary terms differentiate which paper goes with which note.
Bullet items provide additional information about the phenotype and may or may not be present, regardless of the number of papers.
Note: There is also a References section at the bottom of the Phenotypic Allele Detail report. Clicking All references displays links to all citations associated with the allele. Matching items are sorted chronologically with the most recent papers appearing at the top.
Can I see annotations for every checkmarked item in a Genotypes column?
Yes. Click the colored box at the head of the Genotypes row (i.e., hm1, ht4). A new browser tab appears, containing all available phenotypic details by genotype.
- The color assigned to the genotype appears in a small box. The genotype abbreviation appears beneath the box (e.g., hm1). This enables quick identification of genotypes, particularly when opening several tabs for comparison.
- The Allelic Composition and Genetic Background appear in the header. Clicking any allele symbol brings up its Phenotypic Allele Detail report.
- Find Mice:
- A link to the International Mouse Strain Resource (IMSR) where you can search for stocks available from multiple repositores
- Links to stocks listed in the IMSR that contain any of the alleles or transgenes in this genotype, if available
- Links to stocks listed in the IMSR that contain any allele of the gene
- Mouse Models of Human Disease appears if relevant for this genotype.
- When available, images associated with this genotype appear in the top right corner.
- Each affected system (e.g., nervous system) identified by a check mark in the genotype column appears.
- Each system term with an abnormality assertion (e.g., brain inflammation) appears, linked to its term detail report in the Mammalian Phenotype Browser.
- Reference identifiers (e.g., J:120427) appear in parentheses next to the term, linked to the References report.
What else is there to know about genotype windows?
- You can open as many tabs as desired (there is one for every item in the Genotypes row) for data comparisons.
- When available, a table featuring mouse models of human diseases appears last in the display, so if this is your area of interest, be sure to expand (or scroll to the bottom of) genotype windows.
- You can follow Affected system links to the MGI Mammalian Phenotype Browser and see terms represented within the context of phenotype ontology.
Note: This opens a new window.
- You can follow MGI J: numbers to MGI Reference reports to find the research that supports the annotations.
Note: This opens a new window.
What if I'm only interested in disease models?
Scroll down the Allele Detail report to the Disease Models section. A check mark appears in any Genotypes column where there is phenotypic evidence of a disease model. Click the colored box at the top of that column (e.g., cn1) to access phenotypic details.
How do I get rid of extra headers, or subsystem views?
- Click show or hide to expand or collapse data views.
- Click ► or ▼ to open or close just one system. Note: Closing a system also hides the additional labels that appear.
Why aren't all the systems in the Mammalian Phenotype vocabulary listed?
Only those systems with at least one annotation appear in the table.
How can I tell, without opening every window, what alleles and strains are involved with all genotypes?
Scroll down to below the Affected Systems table and click the link to View phenotypes for all genotypes (concatenated display). All genotypes listed in the Phenotypes section appear, paired with their allelic composition and genetic background data. The view of the genotype data is vertical rather than horizontal (as in the Affected Systems table).
Why is the order of systems different in the summary table versus the genotype detail table?
Items in the Affected Systems list on the Phenotypes table are ordered alphabetically.
For any annotated subterms beneath these systems, the order is weighted by importance as specified by MGI curators.
How often are annotations added?
MGI curators add new annotations from the literature every day. The MGI web site is updated with these and other new data once a week.
Are there examples?
- For additional terminology and/or to locate an annotation in the Mammalian Phenotype ontology, click ► to open any affected system, and follow subsystem links to the Mammalian Phenotype Browser term detail reports.
- For the research that supports an annotation, click the header row of interest (e.g., hm1) and expand the window that opens. An MGI J: number (in parentheses) follows each annotation and links to a Reference Detail report.
- To rule out abnormality (for the time being), look at anything marked with N in a given system/subsystem.
- To focus on mutations that affect a disease of interest, locate the Disease Models section of the Allele Detail report. Click Genotypes columns where check marks occur (i.e., hm3). In the window that appears, locate the Mouse Models of Human Disease table at the bottom of that display. Note: The Disease models table at the bottom of the Allele Detail report lists all genotypes evaluated as models of human diseases.